JSON schema: Rnaseq

[jen-reeve]

• Fork the pipeline to your user account, if you have not done so before (Make sure you deselect Copy the master branch only)
• Go to the dev branch and sync the upstream changes (Sync fork -> Update branch)
• Create a branch called json-schema-improvements with the dev branch as base in the fork
• Open the json-schema-improvements branch of the fork either locally (git clone) or online (via Github Codespaces, GitPod...)
• Open the nextflow_schema.json file
• Check that the value in "$schema" is "https://json-schema.org/draft/2020-12/schema". The pipeline should be updated to nf-schema if this is not the case. See the migration guide on how to do this
• Check the schema for insufficient validation keywords and error messages. See the guide for more information on this
• Do the same thing for assets/schema_input.json
• Run nextflow run main.nf -profile test,docker --outdir results -stub to check for any failures in validation with the basic test setup
• Update the changelog of the pipeline
• Push all changes to your fork (if you have not done so yet)
• Open a pull request to the dev branch of the nf-core repository
• Request a review in #hackathon-mar-2025-json-schema-improvements or in the pipeline channel (e.g. #sarek for nf-core/sarek) and set the issue status to Ready to review (PR: )
• Wait for approval and merge the pull request once everything works again
• Set the issue status to Done